Previous Years
- Janice Kielbassa, Ralf Bortfeldt, Stefan Schuster, Ina Koch. Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Computational Biology and Chemistry (2009) 33: 46-61, doi:10.1016/j.compbiolchem.2008.07.022.
- Ina Koch, Georg Fuellen. A review of bioinformatics education in Germany Briefings in Bioinformatics 9(3):232-242 (2008) doi:10.1093/bib/bbn006. PubMed
- Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Bjorn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch. Modularization of biochemical networks based on classification of Petri net t-invariants BMC Bioinformatics 9:90 (2008), doi:10.1186/1471-2105-9-90. PubMed
- Stefanie Grunwald, Astrid Speer, Jörg Ackermann, Ina Koch. Petri net modelling of gene regulation of the Duchenne muscular dystrophy BioSystems 92: 189-205 (2008), doi:10.1016/j.biosystems.2008.02.005. PubMed
- Ina Koch, Monika Heiner. Petri nets In: Analysis of Biological Networks Eds. Björn H. Junker, Falk Schreiber, Wiley Book Series in Bioinformatics (Series Eds. Yi Pan, Albert Y. Zomaya) chapter 7:139-180 (2008).
- Andrea Sackmann, Dorota Formanowicz, Pjotr Formanowicz, Ina Koch, Jacek Blazewicz. An analysis of the Petri net based model of the human body iron homeostasis process Computational Biology and Chemistry 31:1-10 (2007). PubMed
- Andrea Sackmann, Monika Heiner, Ina Koch. Application of Petri net based analysis techniques to signal transduction pathways BMC Bioinformatics 7:482 (2006), doi:10.1186/1471-2105-7-482. PubMed
- Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, Dieter Jahn. JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Nucleic Acids Research 34:W510-W515 (2006). PubMed
- Louchka Popova-Zeugmann, Monika Heiner, Ina Koch. Time Petri Nets for Modelling and Analysis of Biochemical Networks Fundamenta Informaticae 67:149-162 (2005).
- Ina Koch, Björn H. Junker, Monika Heiner. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics 21:1219-1226 (2005). PubMed
- Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser. Columba: an integrated database of proteins, structures, and annotations BMC Bioinformatics 6:81 (2005). PubMed
- Ina Koch, Markus Schüler, Monika Heiner. STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks. In Silico Biol. 5(2):129-37 (2005) PubMed
- Ina Koch, Markus Schüler, Monika Heiner. A Software Tool for Petri Net based based Analysis in Biochemical Networks. In Silico Biology 5, 0014 (2004).
- Louchka Popova-Zeugmann, Monika Heiner, Ina Koch. Modelling and Analysis of Biochemical Networks with Time Petri Nets. Proc. Workshop Concurrency, Specification & Programming 2004, Caputh, Sept. 24 - 26, Informatik-Berichte der HUB Nr. 170, 1:136-143 (2004).
- Ina Koch, Monika Heiner. Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets. Tutorial Notes, 5th Int. Conference on Systems Biology - ICSB 2004, Heidelberg/Germany, October (2004).
- Monika Heiner, Ina Koch. Petri Net Based Model Validation in Systems Biology. Proceedings 25th International Conference on Application and Theory of Petri Nets, ICATPN 2004. July, 21-25, Bologna, Italy, Springer Verlag Berlin LNCS 3099:216-237 (2004).
- Patrick May, Stefan Barthel, Ina Koch. PTGL - Protein Topology Graph Library. Bioinformatics 20(17):3277-3279 (2004). PubMed
- Monika Heiner, Ina Koch, Jürgen Will. Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. Journal BioSystems, 75(1-3):15-28 (2004). PubMed
- Kristian Rother, Heiko Müller, Silke Trissl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser. COLUMBA: Multidimensional Data Integration of Protein Annotations. Proceedings International Workshop of Data Integration in Life Sciences, DILS 2004. March, 25-26, Leipzig, Germany, Springer Verlag Berlin LCBI 2994:156-171 (2004).
- Marco Sifringer, Birgit Uhlenberg, Stefanie Lammel, Rita Hanke, Benjamin Neumann, Arpad von Moers, Ina Koch, Astrid Speer. Identification of transcripts from a subtraction library which might be responsible for the mild phenotype in an intrafamilially variable course of Duchenne muscular dystrophy. Human Molecular Genetics 114:149-156 (2003). PubMed
- Monika Heiner, Ina Koch, Jürgen Will. Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB Proc. - First International Workshop on Computational Methods in Systems Biology, Rovereto, Italy, ed. C. Priami, February 24-26, LNCS2602:173 (2003).
- Christian Köberle, Volker Patzel, Ina Koch. RNA Analysis and Antisense Oligodeoxyribonucleotide Prediction Tool - RAOPT. Currents in Computational Molecular Biology, eds. R. Spang, P. Beziat, M. Vingron. pp. 195-196 (2003).
- Patrick May, Ina Koch. PTGL - Protein Topology Graph Library. ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics; eds. C. Christophe, H.-P- Lenhof, M.-F. Sagot:193-194 (2003).
- Kristian Rother, Silke Trissl, H. Müller, Patrick May, R. Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius Frömmel. Columba - A Database of Annotations of Protein Structure. ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics; eds. C. Christophe, H.-P- Lenhof, M.-F. Sagot:109-110 (2003).
- Klaus Voss, Monika Heiner, Ina Koch. Steady State Analysis of Metabolic Pathways using Petri Nets. In Silico Biology 3(3):367-387 (2003). PubMed
- Evgenia V. Kriventseva, Ina Koch, Rolf Appweiler, Martin Vingron, Peer Bork, Mikhail S. Gelfand, Shamil Sunyaev. Increase of functional diversity by alternative splicing. Trends in Genetics 19:124-128 (2003). PubMed
- Stéphanie Boué, Martin Vingron, Evgenia V. Kriventseva, Ina Koch. Theoretical analysis of alternative splice forms using computational methods. ECCB-European Conference on Computational Biology, Oxford Press, Bioinformatics 18(suppl. 2): S65-S73 (2002). PubMed
- Stefan Schuster, Thomas Pfeiffer, Ina Koch, Ferdinand Moldenhauer, Thomas Dandekar. Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae. Bioinformatics 18(2):351-361 (2002).
- Monika Heiner, Ina Koch, Klaus Voss. Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets. CPN'01-Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, University of Aarhus, Denmark, ed.K. Jensen,ISSN 0105-8517, pp.15-34 (2001).
- Shamil Sunyaev, Vasily Ramensky, Ina Koch, Warren Lathe III, Alexey S. Kondrashov, Peer Bork. Prediction of Deleterious Human Alleles. Human Molecular Genetics 10(6): 591-597 (2001).
- Ina Koch. Fundamental Study: Enumerating all connected maximal common subgraphs in two graphs. Theoretical Computer Science 250:1-30 (2001).
- Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar. Structural Analysis of metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma pneumoniae. Proc.Germ.Conf.Bioinf., eds. E.-B. Bauer, U.Rost, J. Stoye, M. Vingron, October, 5-7 Heidelberg, Germany, (2000), Logos Verlag Berlin, ISBN 3-89722-498-4, pp.115-120 (2000).
- Ina Koch, Stefan Schuster, Monika Heiner. Using time-dependent Petri nets for the analysis of metabolic networks. Workshop Modellierung und Simulation Metabolischer Netzwerke, eds. R. Hofestädt, K. Lautenbach, M. Lange, Preprint No.10, Faculty of Computer Science, Otto-von-Guericke University of Magdeburg, pp.15-21 (2000).
- Ina Koch, Stefan Schuster, Monika Heiner. Simulation and analysis of metabolic networks by time-dependent Petri nets. Computer Science and Biology - Proceedings of the German Conference on Bioinformatics 1999, pp.208-210 (1999).
- Jeff R. O'Connel, Nino Margetic, Martin Farrall, G.M. Lathrop, Daniel E. Weeks, Florence Demenais, Maria Martinez, Gilles Durrieu, Ina Koch, Klaus Rohde. Dissecting complex diseases with FINESSE. Genetic Epidemiology 15:521-522 (1998).
- Ina Koch. Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen. Wissenschaft und Technik Verlag, Berlin, ISBN 3-89685-446-1, (1998).
- Ina Koch, Thomas Lengauer. Detection of distant structural similarities in a set of proteins using a fast graph-based method. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, June, 21-26 (1997) in Halkidiki, Greece. AAAI Press, California. eds. T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, A. Valencia, pp.167-187 (1997).
- Ina Koch, Thomas Lengauer, Egon Wanke. An algorithm for finding maximal common subtopologies in a set of proteins. Journal of Computational Biology 3(2):289-306 (1996).
- Frieder Kaden, Ina Koch, Joachim Selbig. Heuristische Analyse und Vorhersage von Proteinstrukturen. Arbeitspapiere der GMD - Gesellschaft für Mathematik und Datenverarbeitung GmbH, 656 (1992).
- Ina Koch, Frieder Kaden, Joachim Selbig. Analysis of protein sheet topologies by graph-theoretical methods. Proteins: Structure, Function, and Genetics 12:314-324 (1992).
- Joachim Selbig, Frieder Kaden, Ina Koch. Applying machine learning methods for finding significant amino acid properties in proteins. FEBS Letters 297:1-6 (1992).
- Joachim Selbig, Ina Koch, Frieder Kaden. Automatic knowledge acquisition for the prediction of protein structures. Contributions to Artificial Intelligence; eds. U. Geske, D. Koch Akademie-Verlag Berlin, Germany, pp. 109-120 (1991).
- Frieder Kaden, Ina Koch, Joachim Selbig. Knowledge-based prediction of protein structures. Journal of Theoretical Biology 147(1):85-100 (1990).
- Frieder Kaden, Ina Koch, Joachim Selbig. Knowledge-based prediction of protein structures. Report DAI-PEE-1, ZKI - Central Institut for Cybernetics and Information Processes of Academy of Sciences, Berlin, Germany (1989).
- Ina Koch, Ada Markwald. Membranen mit trägergebundenem Transport (Carriermembranen) III. Polymermembranen mit fixierten funktionellen Gruppen. Literaturberichte, Academy of Sciences Berlin, Germany (1986).